Mercurial > repos > bgruening > deeptools_compute_matrix
changeset 14:5335711251f6 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
| author | bgruening |
|---|---|
| date | Sun, 14 May 2017 19:20:26 -0400 |
| parents | 77c614635e16 |
| children | fd1275e01605 |
| files | computeMatrix.xml deepTools_macros.xml repository_dependencies.xml test-data/bamPEFragmentSize_result1.txt test-data/plotFingerprint_quality_metrics.tabular tool_dependencies.xml |
| diffstat | 6 files changed, 51 insertions(+), 64 deletions(-) [+] |
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--- a/computeMatrix.xml Fri Mar 31 18:30:53 2017 -0400 +++ b/computeMatrix.xml Sun May 14 19:20:26 2017 -0400 @@ -7,14 +7,7 @@ <expand macro="requirements" /> <command> <![CDATA[ - #import re - #import tempfile - #set bw_files=[] - #for $counter, $bigwig, in enumerate($scoreFileName): - #set identifier = re.sub('[^\s\w\-]', '_', str($bigwig.element_identifier)) - ln -f -s "${bigwig}" "${identifier}_${counter}.bw" && - #silent $bw_files.append('%s_%s.bw' % ($identifier, $counter)) - #end for + @multiple_input_bigwigs@ #set bed_files=[] #for $counter, $rf, in enumerate($regionsFiles): @@ -28,7 +21,7 @@ $mode.mode_select --regionsFileName '#echo "' '".join($bed_files)#' - --scoreFileName '#echo "' '".join($bw_files)#' + --scoreFileName '#echo "' '".join($files)#' --outFileName '$outFileName' @@ -79,6 +72,9 @@ #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '': --scale $advancedOpt.scale #end if + #if $advancedOpt.samplesLabel is not None and str($advancedOpt.samplesLabel) != '': + --samplesLabel $advancedOpt.samplesLabel + #end if @ADVANCED_OPTS_GTF@ @@ -94,10 +90,7 @@ help="File, in BED format, containing the regions to plot."/> </repeat> - <param name="scoreFileName" format="bigwig" type="data" - label="Score file" multiple="True" - help="You can generate a bigWig file from a BAM file using the - bamCoverage tool. (--scoreFileName)"/> + <expand macro="multiple_input_bigwigs" MIN="1" LABEL="Score file" TITLE="Score files"/> <conditional name="mode" > <param name="mode_select" type="select" @@ -214,6 +207,15 @@ bias the average values. (--maxThreshold)"/> <param name="scale" type="float" optional="True" label="Scaling factor" help="If set, all values are multiplied by this number. (--scale)"/> + <param argument="--samplesLabel" type="text" size="30" + label="Labels for the samples (each bigwig)" + help="The default is to use the history item label. The sample labels should be separated by + spaces and quoted if a label itself contains a space E.g. label-1 "label 2""> + <sanitizer> + <valid initial="string.printable"> + </valid> + </sanitizer> + </param> <expand macro="gtf_options" /> @@ -229,7 +231,7 @@ <tests> <test> <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" /> - <param name="scoreFileName" value="bamCoverage_result4.bw" ftype="bigwig" /> + <param name="bigwigfiles" value="bamCoverage_result4.bw" ftype="bigwig" /> <param name="showAdvancedOpt" value="yes" /> <param name="mode_select" value="reference-point" /> <param name="binSize" value="10" /> @@ -241,7 +243,7 @@ </test> <test> <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" /> - <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" /> + <param name="bigwigfiles" value="computeMatrix2.bw" ftype="bigwig" /> <param name="showAdvancedOpt" value="yes" /> <param name="mode_select" value="reference-point" /> <param name="binSize" value="10" /> @@ -251,7 +253,7 @@ </test> <test> <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" /> - <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" /> + <param name="bigwigfiles" value="computeMatrix2.bw" ftype="bigwig" /> <param name="showAdvancedOpt" value="yes" /> <param name="mode_select" value="scale-regions" /> <param name="endLabel" value="END" />
--- a/deepTools_macros.xml Fri Mar 31 18:30:53 2017 -0400 +++ b/deepTools_macros.xml Sun May 14 19:20:26 2017 -0400 @@ -1,10 +1,9 @@ <macros> <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> - <token name="@WRAPPER_VERSION@">2.5.0</token> + <token name="@WRAPPER_VERSION@">2.5.1.0</token> <xml name="requirements"> <requirements> - <requirement type="package" version="2.7.10">python</requirement> <requirement type="package" version="@WRAPPER_VERSION@">deeptools</requirement> <yield /> </requirements> @@ -25,6 +24,21 @@ </conditional> </xml> + <token name="@PLOTWIDTHHEIGHT@"> + --plotWidth '$advancedOpt.plotWidth' + --plotHeight '$advancedOpt.plotHeight' + </token> + + <xml name="plotWidthHeight" tokens="PLOTWIDTH,PLOTHEIGHT"> + <param argument="--plotHeight" type="float" value="@PLOTHEIGHT@" min="1.0" + label="Plot height" + help="Height in cm. The default for the plot height is @PLOTHEIGHT@ centimeters. The minimum value is 1 cm." /> + + <param argument="--plotWidth" type="float" value="@PLOTWIDTH@" min="1.0" + label="Plot width" + help="Width in cm. The default value is @PLOTWIDTH@ centimeters. The minimum value is 1 cm." /> + </xml> + <token name="@ADVANCED_OPTS_READ_PROCESSING@"> #if $advancedOpt.doExtendCustom.doExtend == 'custom': --extendReads $advancedOpt.doExtendCustom.extendReadsValue @@ -369,46 +383,26 @@ </citations> </xml> - <xml name="multiple_input_bams"> + <xml name="multiple_input_bams" tokens="MIN"> <conditional name="multibam_conditional"> <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below."> <option value="No" selected="true">No</option> <option value="Yes">Yes</option> </param> <when value="No"> - <param argument="--bamfiles" type="data" format="bam" min="1" + <param argument="--bamfiles" type="data" format="bam" min="@MIN@" label="Bam file" multiple="true" help=""/> </when> <when value="Yes"> - <repeat name="multibam_repeats" min="1" title="BAM Files"> + <repeat name="multibam_repeats" min="@MIN@" title="BAM Files"> <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" /> </repeat> </when> </conditional> </xml> - <xml name="multiple_input_bams_min2"> - <conditional name="multibam_conditional"> - <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples -is vital to you, select Yes below."> - <option value="No" selected="true">No</option> - <option value="Yes">Yes</option> - </param> - <when value="No"> - <param argument="--bamfiles" type="data" format="bam" min="2" - label="Bam file" multiple="true" - help=""/> - </when> - <when value="Yes"> - <repeat name="multibam_repeats" min="2" title="BAM Files"> - <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" /> - </repeat> - </when> - </conditional> - </xml> - - <xml name="multiple_input_bigwigs"> + <xml name="multiple_input_bigwigs" tokens="MIN,LABEL,TITLE"> <conditional name="multibigwig_conditional"> <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below."> @@ -416,13 +410,13 @@ <option value="Yes">Yes</option> </param> <when value="No"> - <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2" - label="Bigwig file" - help="A Bigwig file."/> + <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="@MIN@" + label="@LABEL@" + help="You can generate a bigWig file from a BAM file using the bamCoverage tool."/> </when> <when value="Yes"> - <repeat name="multibigwig_repeats" min="2" title="BigWig files"> - <param argument="--bigwigfiles" type="data" format="bigwig" label="Bigwig file" help="A Bigwig file."/> + <repeat name="multibigwig_repeats" min="@MIN@" title="@TITLE@"> + <param argument="--bigwigfiles" type="data" format="bigwig" label="@LABEL@" help="You can generate a bigWig file from a BAM file using the bamCoverage tool."/> </repeat> </when> </conditional> @@ -467,16 +461,16 @@ #import re #if $multibigwig_conditional.orderMatters == "No": #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles): - #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier)) - ln -s "${bigwig}" "${counter}.bw" && - #silent $files.append('%s.bw' % $counter) + #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier)) + ln -f -s "${bigwig}" "${identifier}_${counter}.bw" && + #silent $files.append('%s_%s.bw' % ($identifier, $counter)) #silent $labels.append("'%s'" % $identifier) #end for #else: #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats): #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier)) - ln -s "${f.bigwigfiles}" "${counter}.bw" && - #silent $files.append('%s.bw' % $counter) + ln -f -s "${f.bigwigfiles}" "${identifier}_${counter}.bw" && + #silent $files.append('%s_%s.bw' % ($identifier, $counter)) #silent $labels.append("'%s'" % $identifier) #end for #end if
--- a/repository_dependencies.xml Fri Mar 31 18:30:53 2017 -0400 +++ b/repository_dependencies.xml Sun May 14 19:20:26 2017 -0400 @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories> - <repository changeset_revision="df883cc67fbd" name="data_manager_twobit_builder" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="9946bc39c834" name="data_manager_twobit_builder" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </repositories>
--- a/test-data/bamPEFragmentSize_result1.txt Fri Mar 31 18:30:53 2017 -0400 +++ b/test-data/bamPEFragmentSize_result1.txt Sun May 14 19:20:26 2017 -0400 @@ -1,6 +1,6 @@ -BAM file : 0.bam +Sample label: bowtie2 test1.bam Sample size: 3 Fragment lengths:
--- a/test-data/plotFingerprint_quality_metrics.tabular Fri Mar 31 18:30:53 2017 -0400 +++ b/test-data/plotFingerprint_quality_metrics.tabular Sun May 14 19:20:26 2017 -0400 @@ -1,3 +1,3 @@ Sample AUC Synthetic AUC X-intercept Synthetic X-intercept Elbow Point Synthetic Elbow Point JS Distance Synthetic JS Distance % genome enriched diff. enrichment CHANCE divergence bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 NA 0.269004498068 NA NA NA -bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 NA 0.269004498068 NA NA NA +bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 0.0 0.269004498068 0 0 0
--- a/tool_dependencies.xml Fri Mar 31 18:30:53 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="python" version="2.7.10"> - <repository changeset_revision="bd7165ea6526" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="deeptools" version="2.5.0"> - <repository changeset_revision="72856dd1f9a5" name="package_python_2_7_deeptools_2_5_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>